Hi Ninad, You have downloaded the files you need. A cat of chr*.fa produces hg19.fa the same as if hg19.2bit was converted to hg19.fa.
According to the BWA manual (http://bio-bwa.sourceforge.net/bwa.shtml), the reference needs to be indexed as the first step: "...the database file in the FASTA format must be first indexed with the ‘index’ command..." Make sure you start with this indexing step. Please refer to the BWA manual for further assistance with BWA. Katrina Learned UCSC Genome Bioinformatics Group On 8/19/11 3:37 AM, Ninad Oak wrote: > Respected Sir, > > I want to use hg19.fa file as a reference genome and wish to obtain the same > from UCSC website. > I have a linux i686 machine. I downloaded hg19.2bit file, but the converter > available twoBitToFa on the UCSC site is for linux x86_64 machine. > Then I also tried cat chr*.fa but the hg19 file created is not read by bwa. > > Please help and provide me with the reference genome asap. > Regards, > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
